Yeah, the only case where a sky citie would happen is in that “air whale”, because in that scenario, the metal might float, and swimming through the air is what they have to do. Any other civilitastions that do that are just doing it as a proof of concept (See, I told you we could make a flying city!), or, with that magnetic scenario, but even there, unlikely. The only non air-whale scenario I can think of is a massive metropolis. So massive that the buildings are so tall they collaps under their own weight, so they build buildings on top of them, and make those ones fly. Some with flying roads, others where you have no choice but to use the hover cars! (Patent pending)
So, yeah. Also, like your sky-whale! but, it might be a sky-dolphin… which sounds coller?
And, for the bird civilisations, they might, in flat areas, build their cities on stilts, but yeah, probally jjust like tall areas, with large doors.